1 Introduction

Nucleic acid sequences provide the fundamental starting point for describing
and understanding the structure, function, and development of genetically
diverse organisms. The GenBank, EMBL, and DDBJ nucleic acid sequence data
banks have from their inception used tables of sites and features to describe
the roles and locations of higher order sequence domains and elements within
the genome of an organism.
In February, 1986, GenBank and EMBL began a collaborative effort (joined by
DDBJ in 1987) to devise a common feature table format and common standards for
annotation practice.

2 Overview of the Feature Table format

The overall goal of the feature table design is to provide an extensive
vocabulary for describing features in a flexible framework for manipulating
them. The Feature Table documentation represents the shared rules that allow
the three databases to exchange data on a daily basis.
The range of features to be represented is diverse, including regions which:
* perform a biological function,
* affect or are the result of the expression of a biological function,
* interact with other molecules,
* affect replication of a sequence,
* affect or are the result of recombination of different sequences,
* are a recognizable repeated unit,
* have secondary or tertiary structure,
* exhibit variation, or have been revised or corrected.

2.1 Format Design

The format design is based on a tabular approach and consists of the following
items:
Feature key - a single word or abbreviation indicating functional group
Location - instructions for finding the feature
Qualifiers - auxiliary information about a feature

2.2 Key aspects of this feature table design

* Feature keys allow specific annotation of important sequence features.
* Related features can be easily specified and retrieved.
Feature keys are arranged hierarchically, allowing complex and compound
features to be expressed. Both location operators and the feature keys show
feature relationships even when the features are not contiguous. The hierarchy
of feature keys allows broad categories of biological functionality, such as
rRNAs, to be easily retrieved.
* Generic feature keys provide a means for entering new or undefined features.
A number of "generic" or miscellaneous feature keys have been added to permit
annotation of features that cannot be adequately described by existing feature
keys. These generic feature keys will serve as an intermediate step in the
identification and addition of new feature keys. The syntax has been designed
to allow the addition of new feature keys as they are required.
* More complex locations (fuzzy and alternate ends, for example) can be specified.
Each end point of a feature may be specified as a single point, an alternate
set of possible end points, a base number beyond which the end point lies, or
a region which contains the end point.
* Features can be combined and manipulated in many different ways.
The location field can contain operators or functional descriptors specifying
what must be done to the sequence to reproduce the feature. For example, a
series of exons may be "join"ed into a full coding sequence.
* Standardized qualifiers provide precision and parsibility of descriptive details
A combination of standardized qualifiers and their controlled-vocabulary
values enable free-text descriptions to be avoided.
* The nature of supporting evidence for a feature can be explicitly indicated.
Features, such as open reading frames or sequences showing sequence similarity
to consensus sequences, for which there is no direct experimental evidence can
be annotated. Therefore, the feature table can incorporate contributions from
researchers doing computational analysis of the sequence databases. However,
all features that are supported by experimental data will be clearly marked as
such.
* The table syntax has been designed to be machine parsible.
A consistent syntax allows machine extraction and manipulation of sequences
coding for all features in the table.

2.3 Feature Table Terminology

The format and wording in the feature table use common biological research
terminology whenever possible. For example, an item in the feature table such as:

which might be read as:
This feature, which is a partial coding sequence, is formed by joining
elements indicated to form one contiguous sequence encoding a product called
T-cell receptor beta-chain.
The following sections contain detailed explanations of the feature table
design showing conventions for each component of the feature table, examples
of how the format might be implemented, a description of the exact column
placement of all the data items and examples of complete sequence entries that
have been annotated using the new format. The last section of this document
describes known limitations of the current feature table design.
Appendix I gives an example database entry for the DDBJ, GenBank and EMBL
formats.
Appendices II and III provide reference manuals for the feature table keys and
qualifiers, respectively.
Appendix IV includes controlled vocabularies such as nucleotide base codes,
modified base abbreviations, genetic code tables etc.
This document defines the syntax and vocabulary of the feature table. The
syntax is sufficiently flexible to allow expression of a single biological
entity in numerous ways. In such cases, the annotation staffs at the databases
will propose conventions for standard means of denoting the entities.
This feature table format is shared by GenBank, EMBL and DDBJ. Comments,
corrections, and suggestions may be submitted to any of the database staffs.
New format specifications will be added as needed.

3 Feature table components and format

3.1 Naming conventions

Feature table components, including feature keys, qualifiers, accession
numbers, database name abbreviations, and location operators, are all named
following the same conventions. Component names may be no more than 20
characters long (Feature keys 15, Feature qualifiers 20) and must
contain at least one letter. The following characters are permitted to
occur in feature table component names:
* Uppercase letters (A-Z)
* Lowercase letters (a-z) Numbers (0-9)
* Underscore (_)
* Hyphen (-)
* Single quotation mark or apostrophe (')
* Asterisk (*)

3.2 Feature keys

3.2.1 Purpose

Feature keys indicate
(1) the biological nature of the annotated feature or
(2) information about changes to or other versions of the sequence.
The feature key permits a user to quickly find or retrieve similar features or
features with related functions.

3.2.2 Format and conventions

There is a defined list of allowable feature keys, which is shown in Appendix
II. Each feature must contain a feature key.

3.2.3 Key groups and hierarchy

The feature keys fall into families which are in some sense similar in
function and which are annotated in a similar manner. A functional family may
have a "generic" or miscellaneous key, which can be recognized by the 'misc.'
prefix, that can used for instances not covered by the other defined keys of
that group.
The feature key groups are listed below with a short definition and an
annotation example:
1. Difference and change features
Indicate ways in which a sequence should be changed to produce a different
"version":
misc_difference location
/replace="change_location"
2. Transcript features
Indicate products made by a region:
misc_RNA location
3. Binding features
Indicate that a sequence or nucleotide is covalently, non-covalently, or
otherwise bound to something else:
misc_binding location
/bound_moiety="bound molecule"
4. Repeat features
Indicate repetitive sequence elements:
repeat_region location
5. Recombination features
Indicate regions that have been either inserted or deleted by recombination:
misc_recomb location
6. Structure features
Indicate sequence for which there is secondary or tertiary structural
information:
misc_structure location

3.2.4 Feature key examples

3.3 Qualifiers

3.3.1 Purpose

Qualifiers provide a general mechanism for supplying information about
features in addition to that conveyed by the key and location.

3.3.2 Format and conventions

Qualifiers take the form of a slash (/) followed by the qualifier name and, if
applicable, an equal sign (=) and a value. Each qualifier should have a single
value; if multiple values are necessary, these should be represented by
iterating the same qualifier, eg:

If the location descriptor does not need a continuation line, the first
qualifier begins a new line in the feature location column. If the location
descriptor requires a continuation line, the first qualifier may follow
immediately after the location. Any necessary continuation lines begin in the
same column. See Section 4 for a complete description of data item positions.

3.3.3 Qualifier values

Since qualifiers convey many different types of information, there are several value formats:
1. Free text
2. Controlled vocabulary or enumerated values
3. Citation or reference numbers
4. Sequences

3.3.3.1 Free text

Most qualifier values will be a descriptive text phrase which must be enclosed
in double quotation marks. When the text occupies more than one line, a single
set of quotation marks is required at the beginning and at the end of the
text. The text itself may be composed of any printable characters (ASCII
values 32-126 decimal). If double quotation marks are used within a free text
string, each set (") must be 'escaped' by placing a second double quotation

mark immediately before it (""). For example:
/note="This is an example of ""escaped"" quotation marks"

3.3.3.2 Controlled vocabulary or enumerated values

Some qualifiers require values from a controlled vocabulary and are entered
without quotation marks. For example, the '/direction' qualifier has only
three values: 'left', 'right' or 'both'. Qualifier value controlled
vocabularies, like feature table component names, must be treated as
completely case insensitive: they may be entered and displayed in any
combination of upper and lower case ('/direction=Left' '/direction=left' and
'/direction=LEFT' are all legal and all convey the same meaning). The database
staffs reserve the right to regularize the case of qualifier values. Qualifier
value controlled vocabularies will be maintained by the cooperating database
staffs. Examples of controlled vocabularies can be found in Appendices IV and
V. The database staff should be contacted for the current lists.

3.3.3.3 Citation or reference numbers

The citation or published reference number (as enumerated in the entry
'REFERENCE' or 'RN' data item) should be enclosed in square brackets
(e.g., [3]) to distinguish it from other numbers.

3.3.3.4 Sequences

Literal sequence of nucleotide bases e.g., join(12..45,"atgcatt",988..1050) in
location descriptors has become illegal starting from implementation of
version 2.1 of the Feature Table Definition Document (December 15, 1998)

3.4 Location

3.4.1 Purpose

The location indicates the region of the presented sequence which corresponds
to a feature.

3.4.2 Format and conventions

The location contains at least one sequence location descriptor and may
contain one or more operators with one or more sequence location descriptors.
Base numbers refer to the numbering in the entry. This numbering designates
the first base (5' end) of the presented sequence as base 1.
Base locations beyond the range of the presented sequence may not be used in
location descriptors, the only exception being location in a remote entry (see
3.4.2.1, e).
Location operators and descriptors are discussed in more detail below.

3.4.2.1 Location descriptors

The location descriptor can be one of the following:
(a) a single base number
(b) a site between two indicated adjoining bases
(c) a single base chosen from within a specified range of bases (not allowed
for new entries)
(d) the base numbers delimiting a sequence span
(e) a remote entry identifier followed by a local location descriptor
(i.e., a-d)
A site between two adjoining nucleotides, such as endonucleolytic cleavage
site, is indicated by listing the two points separated by a carat (^). The
permitted formats for this descriptor are n^n+1 (for example 55^56), or, for
circular molecules, n^1, where "n" is the full length of the molecule, ie
1000^1 for circular molecule with length 1000.
A single base chosen from a range of bases is indicated by the first base
number and the last base number of the range separated by a single period
(e.g., '12.21' indicates a single base taken from between the indicated
points). From October 2006 the usage of this descriptor is restricted :
it is illegal to use "a single base from a range" (c) either on its own or
in combination with the "sequence span" (d) descriptor for newly created entries.
The existing entries where such descriptors exist are going to be retrofitted.
Sequence spans are indicated by the starting base number and the ending base
number separated by two periods (e.g., '34..456'). The '<' and '>' symbols may
be used with the starting and ending base numbers to indicate that an end
point is beyond the specified base number. The starting and ending base
positions can be represented as distinct base numbers ('34..456') or a site
between two indicated adjoining bases.
A location in a remote entry (not the entry to which the feature table
belongs) can be specified by giving the accession-number and sequence version
of the remote entry, followed by a colon ":", followed by a location
descriptor which applies to that entry's sequence (i.e. J12345.1:1..15, see
also examples below)

3.4.2.2 Operators

The location operator is a prefix that specifies what must be done to the
indicated sequence to find or construct the location corresponding to the
feature. A list of operators is given below with their definitions and most
common format.
complement(location)
Find the complement of the presented sequence in the span specified by
"location" (i.e., read the complement of the presented strand in its 5'-to-3'
direction)
join(location,location, ... location)
The indicated elements should be joined (placed end-to-end) to form one
contiguous sequence
order(location,location, ... location)
The elements can be found in the
specified order (5' to 3' direction), but nothing is implied about the
reasonableness about joining them
Note : location operator "complement" can be used in combination with either "
join" or "order" within the same location; combinations of "join" and "order"
within the same location (nested operators) are illegal.

3.4.3 Location examples

The following is a list of common location descriptors with their meanings:

Location Description
467 Points to a single base in the presented sequence
340..565 Points to a continuous range of bases bounded by and
including the starting and ending bases
<345..500 Indicates that the exact lower boundary point of a feature
is unknown. The location begins at some base previous to
the first base specified (which need not be contained in
the presented sequence) and continues to and includes the
ending base
<1..888 The feature starts before the first sequenced base and
continues to and includes base 888
1..>888 The feature starts at the first sequenced base and
continues beyond base 888
102.110 Indicates that the exact location is unknown but that it is
one of the bases between bases 102 and 110, inclusive
123^124 Points to a site between bases 123 and 124
join(12..78,134..202) Regions 12 to 78 and 134 to 202 should be joined to form
one contiguous sequence
complement(34..126) Start at the base complementary to 126 and finish at the
base complementary to base 34 (the feature is on the strand
complementary to the presented strand)
complement(join(2691..4571,4918..5163))
Joins regions 2691 to 4571 and 4918 to 5163, then
complements the joined segments (the feature is on the
strand complementary to the presented strand)
join(complement(4918..5163),complement(2691..4571))
Complements regions 4918 to 5163 and 2691 to 4571, then
joins the complemented segments (the feature is on the
strand complementary to the presented strand)
J00194.1:100..202 Points to bases 100 to 202, inclusive, in the entry (in
this database) with primary accession number 'J00194'
join(1..100,J00194.1:100..202)
Joins region 1..100 of the existing entry with the region
100..202 of remote entry J00194

4 Feature table Format

The examples below show the preferred sequence annotations for a number of
commonly occurring sequence types. These examples may not be appropriate in
all cases but should be used as a guide whenever possible. This section
describes the columnar format used to write this feature table in "flat-file"
form for distributions of the database.

4.2 Definition of line types

The feature table consists of a header line, which contains the column titles
for the table, and the individual feature entries. Each feature entry is
composed of a feature descriptor line and qualifier and continuation lines,
if needed. The feature descriptor line contains the feature's name, key, and
location. If the location cannot be contained on the first line of the feature
descriptor, it is continued on a continuation line immediately following the
descriptor line. If the feature requires further attributes, feature qualifier
lines immediately follow the corresponding feature descriptor line (or its
continuation). Qualifier information that cannot be contained on one line
continues on the following continuation lines as necessary.

4.3 Data item positions

Data on the qualifier and continuation lines begins in column position 22 (the
first 21 columns contain blanks). The EMBL format for all lines differs from
the GenBank / DDBJ formats that it includes a line type abbreviation in
columns 1 and 2.

4.4 Use of blanks

Blanks (spaces) may, in general, be used within the feature location and
qualifier values to make the construction more readable. The following rules
should be observed:
* Names of feature table components may not contain blanks (see Section 3.1)
* Operator names may not be separated from the following open parenthesis (the
beginning of the operand list) by blanks.
* Qualifiers may not be separated from the preceding slash or the following
equals sign (if one) by blanks

5 Examples of sequence annotation

The examples below show the preferred sequence annotations for a number of
commonly occurring sequence types. These examples may not be appropriate in
all cases but should be used as a guide whenever possible.

6 Limitations of this feature table design

During the development of the feature table design numerous choices between
simplicity and representational power had to be made. In order to create a
design which was capable of representing the most common features of
biological significance, a certain degree of complexity in the syntax was
guaranteed. However, to limit that level of complexity, certain limitations of
the design syntax have been accepted.

7.2 Appendix II: Feature keys reference

The following has been organized according to the following format:
Feature Key the feature key name
Definition the definition of the key
Mandatory qualifiers qualifiers required with the key; if there are no
mandatory qualifiers, this field is omitted.
Optional qualifiers optional qualifiers associated with the key
Organism scope valid organisms for the key; if the scope is any
organism, this field is omitted.
Molecule scope valid molecule types; if the scope is any molecule
type, this field is omitted.
References citations of published reports, usually supporting the
feature consensus sequence
Comment comments and clarifications
Abbreviations:
accnum an entry primary accession number
<amino_acid> abbreviation for amino acid
<base_range> location descriptor for a simple range of bases
<bool> Boolean truth value. Valid values are yes and no
<integer> unsigned integer value
<location> general feature location descriptor
<modified_base> abbreviation for modified nucleotide base
[number] integer representing number of citation in entry's
reference list
<repeat_type> value indicating the organization of a repeated
sequence.
"text" any text or character string. Since the string is
delimited by double quotes, double quotes may only
appear as part of the string if they appear in pairs.
For example, the sentence:
The "label" qualifier is no longer legal.
would be formatted thus:
"The ""label"" qualifier is no longer legal."

Feature Key assembly_gap
Definition gap between two components of a genome or transcriptome
assembly;
Mandatory qualifiers /estimated_length=unknown or <integer>
/gap_type="TYPE"
/linkage_evidence="TYPE" (Note: Mandatory only if the
/gap_type is "within scaffold" or "repeat within scaffold".
If there are multiple types of linkage_evidence, they
will appear as multiple /linkage_evidence="TYPE" qualifiers.
For all other types of assembly_gap features, use of
the /linkage_evidence qualifier is invalid.)
Mandatory qualifiers under assembly_gap feature for transcriptome
shotgun assemblies (TSA):
/estimated_length=<integer>
/gap_type="within scaffold" and /linkage_evidence="TYPE"
where TYPE can not be "unspecified";
Comment the location span of the assembly_gap feature for an unknown gap has
to be specified by the submitter; the specified gap length has to be
reasonable (less or = 1000) and will be indicated as "n"'s in sequence.
However, the value for the estimated_length of assembly_gap features
within a single (non-CON) transcriptome record must be an integer
and can not be "unknown";

Feature Key CDS
Definition coding sequence; sequence of nucleotides that
corresponds with the sequence of amino acids in a
protein (location includes stop codon);
feature includes amino acid conceptual translation.
Optional qualifiers /allele="text"
/artificial_location="[artificial_location_value]"
/citation=[number]
/codon_start=<1 or 2 or 3>
/db_xref="<database>:<identifier>"
/EC_number="text"
/exception="[exception_value]"
/experiment="[CATEGORY:]text"
/function="text"
/gene="text"
/gene_synonym="text"
/inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]"
/locus_tag="text" (single token)
/map="text"
/note="text"
/number=unquoted text (single token)
/old_locus_tag="text" (single token)
/operon="text"
/product="text"
/protein_id="<identifier>"
/pseudo
/pseudogene="TYPE"
/ribosomal_slippage
/standard_name="text"
/translation="text"
/transl_except=(pos:<base_range>,aa:<amino_acid>)
/transl_table=<integer>
/trans_splicing
Comment /codon_start has valid value of 1 or 2 or 3, indicating
the offset at which the first complete codon of a coding
feature can be found, relative to the first base of
that feature;
/transl_table defines the genetic code table used if
other than the universal genetic code table;
genetic code exceptions outside the range of the specified
tables is reported in /transl_except qualifier;
/protein_id consists of a stable ID portion (3+5 format
with 3 position letters and 5 numbers) plus a version
number after the decimal point; when the protein
sequence encoded by the CDS changes, only the version
number of the /protein_id value is incremented; the
stable part of the /protein_id remains unchanged and as
a result will permanently be associated with a given
protein;

Feature Key centromere
Definition region of biological interest identified as a centromere and
which has been experimentally characterized;
Optional qualifiers /citation=[number]
/db_xref="<database>:<identifier>"
/experiment="[CATEGORY:]text"
/inference="[CATEGORY:]TYPE[(same species)][:EVIDENCE_BASIS]"
/note="text"
/standard_name="text"
Comment the centromere feature describes the interval of DNA
that corresponds to a region where chromatids are held
and a kinetochore is formed

Feature Key D-loop
Definition displacement loop; a region within mitochondrial DNA in
which a short stretch of RNA is paired with one strand
of DNA, displacing the original partner DNA strand in
this region; also used to describe the displacement of a
region of one strand of duplex DNA by a single stranded
invader in the reaction catalyzed by RecA protein
Optional qualifiers /allele="text"
/citation=[number]
/db_xref="<database>:<identifier>"
/experiment="[CATEGORY:]text"
/gene="text"
/gene_synonym="text"
/inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]"
/locus_tag="text" (single token)
/map="text"
/note="text"
/old_locus_tag="text" (single token)
Molecule scope DNA

Feature Key gap
Definition gap in the sequence
Mandatory qualifiers /estimated_length=unknown or <integer>
Optional qualifiers /experiment="[CATEGORY:]text"
/inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]"
/map="text"
/note="text"
Comment the location span of the gap feature for an unknown
gap is 100 bp, with the 100 bp indicated as 100 "n"'s in
the sequence. Where estimated length is indicated by
an integer, this is indicated by the same number of
"n"'s in the sequence.
No upper or lower limit is set on the size of the gap.

Feature Key gene
Definition region of biological interest identified as a gene
and for which a name has been assigned;
Optional qualifiers /allele="text"
/citation=[number]
/db_xref="<database>:<identifier>"
/experiment="[CATEGORY:]text"
/function="text"
/gene="text"
/gene_synonym="text"
/inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]"
/locus_tag="text" (single token)
/map="text"
/note="text"
/old_locus_tag="text" (single token)
/operon="text"
/product="text"
/pseudo
/pseudogene="TYPE"
/phenotype="text"
/standard_name="text"
/trans_splicing
Comment the gene feature describes the interval of DNA that
corresponds to a genetic trait or phenotype; the feature is,
by definition, not strictly bound to it's positions at the
ends; it is meant to represent a region where the gene is
located.

Feature Key misc_feature
Definition region of biological interest which cannot be described
by any other feature key; a new or rare feature;
Optional qualifiers /allele="text"
/citation=[number]
/db_xref="<database>:<identifier>"
/experiment="[CATEGORY:]text"
/function="text"
/gene="text"
/gene_synonym="text"
/inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]"
/locus_tag="text" (single token)
/map="text"
/note="text"
/number=unquoted text (single token)
/old_locus_tag="text" (single token)
/phenotype="text"
/product="text"
/pseudo
/pseudogene="TYPE"
/standard_name="text"
Comment this key should not be used when the need is merely to
mark a region in order to comment on it or to use it in
another feature's location

Feature Key operon
Definition region containing polycistronic transcript including a
cluster of genes that are under the control of the same
regulatory sequences/promoter and in the same biological
pathway
Mandatory qualifiers /operon="text"
Optional qualifiers /allele="text"
/citation=[number]
/db_xref="<database>:<identifier>"
/experiment="[CATEGORY:]text"
/function="text"
/inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]"
/map="text"
/note="text"
/phenotype="text"
/pseudo
/pseudogene="TYPE"
/standard_name="text"

Feature Key oriT
Definition origin of transfer; region of a DNA molecule where transfer is
initiated during the process of conjugation or mobilization
Optional qualifiers /allele="text"
/bound_moiety="text"
/citation=[number]
/db_xref="<database>:<identifier>"
/direction=value
/experiment="[CATEGORY:]text"
/gene="text"
/gene_synonym="text"
/inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]"
/locus_tag="text" (single token)
/map="text"
/note="text"
/old_locus_tag="text" (single token)
/rpt_family="text"
/rpt_type=<repeat_type>
/rpt_unit_range=<base_range>
/rpt_unit_seq="text"
/standard_name="text"
Molecule Scope DNA
Comment rep_origin should be used for origins of replication;
/direction has legal values RIGHT, LEFT and BOTH, however only
RIGHT and LEFT are valid when used in conjunction with the oriT
feature;
origins of transfer can be present in the chromosome;
plasmids can contain multiple origins of transfer

Feature Key primer_bind
Definition non-covalent primer binding site for initiation of
replication, transcription, or reverse transcription;
includes site(s) for synthetic e.g., PCR primer elements;
Optional qualifiers /allele="text"
/citation=[number]
/db_xref="<database>:<identifier>"
/experiment="[CATEGORY:]text"
/gene="text"
/gene_synonym="text"
/inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]"
/locus_tag="text" (single token)
/map="text"
/note="text"
/old_locus_tag="text" (single token)
/standard_name="text"
/PCR_conditions="text"
Comment used to annotate the site on a given sequence to which a primer
molecule binds - not intended to represent the sequence of the
primer molecule itself; PCR components and reaction times may
be stored under the "/PCR_conditions" qualifier;
since PCR reactions most often involve pairs of primers,
a single primer_bind key may use the order() operator
with two locations, or a pair of primer_bind keys may be
used.

Feature Key STS
Definition sequence tagged site; short, single-copy DNA sequence
that characterizes a mapping landmark on the genome and
can be detected by PCR; a region of the genome can be
mapped by determining the order of a series of STSs;
Optional qualifiers /allele="text"
/citation=[number]
/db_xref="<database>:<identifier>"
/experiment="[CATEGORY:]text"
/gene="text"
/gene_synonym="text"
/inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]"
/locus_tag="text" (single token)
/map="text"
/note="text"
/old_locus_tag="text" (single token)
/standard_name="text"
Molecule scope DNA
Parent key misc_binding
Comment STS location to include primer(s) in primer_bind key or
primers.

Feature Key telomere
Definition region of biological interest identified as a telomere
and which has been experimentally characterized;
Optional qualifiers /citation=[number]
/db_xref="<database>:<identifier>"
/experiment="[CATEGORY:]text"/note="text"
/inference="[CATEGORY:]TYPE[(same species)][:EVIDENCE_BASIS]"
/note="text"
/rpt_type=<repeat_type>
/rpt_unit_range=<base_range>
/rpt_unit_seq="text"
/standard_name="text"
Comment the telomere feature describes the interval of DNA
that corresponds to a specific structure at the end of
the linear eukaryotic chromosome which is required for
the integrity and maintenance of the end; this region
is unique compared to the rest of the chromosome and
represent the physical end of the chromosome;

Feature Key unsure
Definition a small region of sequenced bases, generally 10 or fewer in its length, which
could not be confidently identified. Such a region might contain called bases
(A, T, G, or C), or a mixture of called-bases and uncalled-bases ('N').
The unsure feature should not be used when annotating gaps in genome assemblies.
Please refer to assembly_gap feature for gaps within the sequence of an assembled
genome. For annotation of gaps in other sequences than assembled genomes use the
gap feature.
Optional qualifiers /allele="text"
/citation=[number]
/compare=[accession-number.sequence-version]
/db_xref="<database>:<identifier>"
/experiment="[CATEGORY:]text"
/gene="text"
/gene_synonym="text"
/inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]"
/locus_tag="text" (single token)
/map="text"
/note="text"
/old_locus_tag="text" (single token)
/replace="text"
Comment use /replace="" to annotate deletion, e.g.
unsure 11..15
/replace=""

Feature Key 3'UTR
Definition 1) region at the 3' end of a mature transcript (following
the stop codon) that is not translated into a protein;
2) region at the 3' end of an RNA virus (following the last
stop codon) that is not translated into a protein;
Optional qualifiers /allele="text"
/citation=[number]
/db_xref="<database>:<identifier>"
/experiment="[CATEGORY:]text"
/function="text"
/gene="text"
/gene_synonym="text"
/inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]"
/locus_tag="text" (single token)
/map="text"
/note="text"
/old_locus_tag="text" (single token)
/standard_name="text"
/trans_splicing

Feature Key 5'UTR
Definition 1) region at the 5' end of a mature transcript (preceding
the initiation codon) that is not translated into a protein;
2) region at the 5' end of an RNA virus genome (preceding the
first initiation codon) that is not translated into a protein;
Optional qualifiers /allele="text"
/citation=[number]
/db_xref="<database>:<identifier>"
/experiment="[CATEGORY:]text"
/function="text"
/gene="text"
/gene_synonym="text"
/inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]"
/locus_tag="text" (single token)
/map="text"
/note="text"
/old_locus_tag="text" (single token)
/standard_name="text"
/trans_splicing

7.3 Appendix III: Summary of qualifiers for feature keys

7.3.1 Qualifier List

The following is a list of available qualifiers for feature keys and their usage.
The information is arranged as follows:
Qualifier name of qualifier; qualifier requires a value if followed by an equal
sign
Definition definition of the qualifier
Value format format of value, if required
Example example of qualifier with value
Comment comments, questions and clarifications

Qualifier /allele=
Definition name of the allele for the given gene
Value format "text"
Example /allele="adh1-1"
Comment all gene-related features (exon, CDS etc) for a given
gene should share the same /allele qualifier value;
the /allele qualifier value must, by definition, be
different from the /gene qualifier value; when used with
the variation feature key, the allele qualifier value
should be that of the variant.

Qualifier /anticodon=
Definition location of the anticodon of tRNA and the amino acid for which
it codes
Value format (pos:<location>,aa:<amino_acid>,seq:<text>) where location is
the position of the anticodon and amino_acid is the abbreviation
for the amino acid encoded and seq is the sequence of the anticodon
Example /anticodon=(pos:34..36,aa:Phe,seq:aaa)
/anticodon=(pos:join(5,495..496),aa:Leu,seq:taa)
/anticodon=(pos:complement(4156..4158),aa:Gln,seq:ttg)

Qualifier /artificial_location
Definition indicates that location of the CDS or mRNA is modified to adjust
for the presence of a frameshift or internal stop codon and not
because of biological processing between the regions.
Value format "heterogeneous population sequenced", "low-quality sequence region"
Example /artificial_location="heterogeneous population sequenced"
/artificial_location="low-quality sequence region"
Comment expected to be used only for genome-scale annotation.

Qualifier /bio_material=
Definition identifier for the biological material from which the nucleic
acid sequenced was obtained, with optional institution code and
collection code for the place where it is currently stored.
Value format "[<institution-code>:[<collection-code>:]]<material_id>"
Example /bio_material="CGC:CB3912" <- Caenorhabditis stock centre
Comment the bio_material qualifier should be used to annotate the
identifiers of material in biological collections that are not
appropriate to annotate as either /specimen_voucher or
/culture_collection; these include zoos and aquaria, stock
centres, seed banks, germplasm repositories and DNA banks;
material_id is mandatory, institution_code and collection_code
are optional; institution code is mandatory where collection
code is present; institution code and collection code are taken
from a controlled vocabulary maintained by the INSDC.

Qualifier /bound_moiety=
Definition name of the molecule/complex that may bind to the
given feature
Value format "text"
Example /bound_moiety="GAL4"
Comment A single /bound_moiety qualifier is legal on the "misc_binding",
"oriT" and "protein_bind" features.

Qualifier /cell_line=
Definition cell line from which the sequence was obtained
Value format "text"
Example /cell_line="MCF7"

Qualifier /citation=
Definition reference to a citation listed in the entry reference field
Value format [integer-number] where integer-number is the number of the
reference as enumerated in the reference field
Example /citation=[3]
Comment used to indicate the citation providing the claim of and/or
evidence for a feature; brackets are used for conformity.

Qualifier /clone=
Definition clone from which the sequence was obtained
Value format "text"
Example /clone="lambda-hIL7.3"
Comment not more than one clone should be specified for a given source
feature; to indicate that the sequence was obtained from
multiple clones, multiple source features should be given.

Qualifier /codon_start=
Definition indicates the offset at which the first complete codon of a
coding feature can be found, relative to the first base of that
feature.
Value format 1 or 2 or 3
Example /codon_start=2

Qualifier /collection_date=
Definition The date on which the specimen was collected.
Date/time ranges are supported by providing two collection dates from among
the supported value formats, delimited by a forward-slash character.
Collection times are supported by adding "T", then the hour, minute and
second, after the date.
Collection times must be in Coordinated Universal Time (UTC), otherwise
known as "Zulu Time" (Z).
Value format "DD-Mmm-YYYY", "Mmm-YYYY", "YYYY"
"YYYY-MM-DDThh:mmZ", "YYYY-MM-DDThh:mm:ssZ", "YYYY-MM-DDThhZ", "YYYY-MM-DD", or "YYYY-MM"
Example /collection_date="21-Oct-1952"
/collection_date="Oct-1952"
/collection_date="1952"
/collection_date="1952-10-21T11:43Z"
/collection_date="1952-10-21T11Z"
/collection_date="1952-10-21"
/collection_date="1952-10"
/collection_date="21-Oct-1952/15-Feb-1953"
/collection_date="Oct-1952/Feb-1953"
/collection_date="1952/1953"
/collection_date="1952-10-21/1953-02-15"
/collection_date="1952-10/1953-02"
/collection_date="1952-10-21T11:43Z/1952-10-21T17:43Z"
/collection_date="2015-10-11T17:53:03Z"
Comment 'Mmm' represents a three-letter month abbreviation, and can be one of
the following: Jan, Feb, Mar, Apr, May, Jun, Jul, Aug, Sep, Oct, Nov, Dec
'YYYY' is a four-digit value representing the year.
'MM' is a two-digit value representing the month.
'DD' is a two-digit value representing the day of the month.
'hh' is a two-digit value representing the hour of the day (00 to 23)
'mm' is a two-digit value representing the minute of the hour (00 to 59)
'ss' is a two-digit value representing the second of the hour (00 to 59)
Within a date range, value formats that make use of 'Mmm' (month
abbreviations) cannot be combined with value formats that make use of
'MM' (two-digit month number)
Collection dates that are specified to at least the month, day, and year
(DD-Mmm-YYYY or YYYY-MM-DD) are strongly encouraged. If the day and/or
month of the collection date are not known, Mmm-YYYY or YYYY-MM or YYYY
may be used.
Within a collection date range, the first date (possibly including time)
must be prior to the second date (possibly including time).
Within a collection date range for which the day, month, and year are
identical, the first time value must be prior to the second time value.

Qualifier /compare=
Definition Reference details of an existing public INSD entry
to which a comparison is made
Value format [accession-number.sequence-version]
Example /compare=AJ634337.1
Comment This qualifier may be used on the following features:
misc_difference, unsure, old_sequence and variation.
The feature "old_sequence" must have either a
/citation or a /compare qualifier. Multiple /compare
qualifiers with different contents are allowed within a
single feature.
This qualifier is not intended for large-scale annotation
of variations, such as SNPs.

Qualifier /country=
Definition locality of isolation of the sequenced organism indicated in
terms of political names for nations, oceans or seas, followed
by regions and localities
Value format "<country_value>[:<region>][, <locality>]" where
country_value is any value from the controlled vocabulary at
http://www.insdc.org/documents/country-qualifier-vocabulary
Example /country="Canada:Vancouver"
/country="France:Cote d'Azur, Antibes"
/country="Atlantic Ocean:Charlie Gibbs Fracture Zone"
Comment Intended to provide a reference to the site where the source
organism was isolated or sampled. Regions and localities should
be indicated where possible. Note that the physical geography of
the isolation or sampling site should be represented in
/isolation_source.

Qualifier /culture_collection=
Definition institution code and identifier for the culture from which the
nucleic acid sequenced was obtained, with optional collection
code.
Value format "<institution-code>:[<collection-code>:]<culture_id>"
Example /culture_collection="ATCC:26370"
Comment the /culture_collection qualifier should be used to annotate
live microbial and viral cultures, and cell lines that have been
deposited in curated culture collections; microbial cultures in
personal or laboratory collections should be annotated in strain
qualifiers;
annotation with a culture_collection qualifier implies that the
sequence was obtained from a sample retrieved (by the submitter
or a collaborator) from the indicated culture collection, or
that the sequence was obtained from a sample that was deposited
(by the submitter or a collaborator) in the indicated culture
collection; annotation with more than one culture_collection
qualifier indicates that the sequence was obtained from a sample
that was deposited (by the submitter or a collaborator) in more
than one culture collection.
culture_id and institution_code are mandatory, collection_code
is optional; institution code and collection code are taken
from a controlled vocabulary maintained by the INSDC.
http://www.insdc.org/controlled-vocabulary-culturecollection-qualifier

Qualifier /db_xref=
Definition database cross-reference: pointer to related information in
another database.
Value format "<database:identifier>" where database is
the name of the database containing related information, and
identifier is the internal identifier of the related information
according to the naming conventions of the cross-referenced
database.
Example /db_xref="UniProtKB/Swiss-Prot:P28763"
Comment the complete list of allowed database types is kept at
http://www.insdc.org/db_xref.html

Qualifier /dev_stage=
Definition if the sequence was obtained from an organism in a specific
developmental stage, it is specified with this qualifier
Value format "text"
Example /dev_stage="fourth instar larva"

Qualifier /direction=
Definition direction of DNA replication
Value format left, right, or both where left indicates toward the 5' end of
the entry sequence (as presented) and right indicates toward
the 3' end
Example /direction=LEFT

Qualifier /EC_number=
Definition Enzyme Commission number for enzyme product of sequence
Value format "text"
Example /EC_number="1.1.2.4"
/EC_number="1.1.2.-"
/EC_number="1.1.2.n"
Comment valid values for EC numbers are defined in the list prepared by the
Nomenclature Committee of the International Union of Biochemistry and
Molecular Biology (NC-IUBMB) (published in Enzyme Nomenclature 1992,
Academic Press, San Diego, or a more recent revision thereof).
The format represents a string of four numbers separated by full
stops; up to three numbers starting from the end of the string can
be replaced by dash "." to indicate uncertain assignment.
Symbol "n" can be used in the last position instead of a number
where the EC number is awaiting assignment. Please note that such
incomplete EC numbers are not approved by NC-IUBMB.

Qualifier /ecotype=
Definition a population within a given species displaying genetically
based, phenotypic traits that reflect adaptation to a local habitat.
Value Format "text"
Example /ecotype="Columbia"
Comment an example of such a population is one that has adapted hairier
than normal leaves as a response to an especially sunny habitat.
'Ecotype' is often applied to standard genetic stocks of
Arabidopsis thaliana, but it can be applied to any sessile
organism.

Qualifier /environmental_sample
Definition identifies sequences derived by direct molecular
isolation from a bulk environmental DNA sample
(by PCR with or without subsequent cloning of the
product, DGGE, or other anonymous methods) with no
reliable identification of the source organism.
Environmental samples include clinical samples,
gut contents, and other sequences from anonymous
organisms that may be associated with a particular
host. They do not include endosymbionts that can be
reliably recovered from a particular host, organisms
from a readily identifiable but uncultured field sample
(e.g., many cyanobacteria), or phytoplasmas that can be
reliably recovered from diseased plants (even though
these cannot be grown in axenic culture).
Value format none
Example /environmental_sample
Comment used only with the source feature key; source feature
keys containing the /environmental_sample qualifier
should also contain the /isolation_source qualifier.
entries including /environmental_sample must not include
the /strain qualifier

Qualifier /exception=
Definition indicates that the coding region cannot be translated using
standard biological rules
Value format "RNA editing", "reasons given in citation",
"rearrangement required for product",
"annotated by transcript or proteomic data"
Example /exception="RNA editing"
/exception="reasons given in citation"
/exception="rearrangement required for product"
/exception="annotated by transcript or proteomic data"
Comment only to be used to describe biological mechanisms such
as RNA editing; where the exception cannot easily be described
a published citation must be referred to; protein translation of
/exception CDS will be different from the according conceptual
translation;
- An /inference qualifier should accompany any use of
/exception="annotated by transcript or proteomic data", to
provide support for the existence of the transcript/protein.
- must not be used where transl_except would be adequate,
e.g. in case of stop codon completion use:
/transl_except=(pos:6883,aa:TERM)
/note="TAA stop codon is completed by addition of 3' A residues to
mRNA".
- must not be used for ribosomal slippage, instead use join operator,
e.g.: CDS join(486..1784,1787..4810)
/note="ribosomal slip on tttt sequence at 1784..1787"

Qualifier /experiment=
Definition a brief description of the nature of the experimental
evidence that supports the feature identification or assignment.
Value format "[CATEGORY:]text"
where CATEGORY is one of the following:
"COORDINATES" support for the annotated coordinates
"DESCRIPTION" support for a broad concept of function such as
that based on phenotype, genetic approach, biochemical function,
pathway information, etc.
"EXISTENCE" support for the known or inferred existence of the
product where text is free text (see examples)
Example /experiment="5' RACE"
/experiment="Northern blot [DOI: 12.3456/FT.789.1.234-567.2010]"
/experiment="heterologous expression system of Xenopus laevis
oocytes [PMID: 12345678, 10101010, 987654]"
/experiment="COORDINATES: 5' and 3' RACE"
Comment detailed experimental details should not be included, and would
normally be found in the cited publications; PMID, DOI and any
experimental database ID is allowed to be used in /experiment
qualifier; value "experimental evidence, no additional details
recorded" was used to replace instances of /evidence=EXPERIMENTAL
in December 2005

Qualifier /focus
Definition identifies the source feature of primary biological
interest for records that have multiple source features
originating from different organisms and that are not
transgenic.
Value format none
Example /focus
Comment the source feature carrying the /focus qualifier
identifies the main organism of the entry, this
determines: a) the name displayed in the organism
lines, b) if no translation table is specified, the
translation table, c) the DDBJ/EMBL/GenBank taxonomic
division in which the entry will appear; only one
source feature with /focus is allowed in an entry; the
/focus and /transgenic qualifiers are mutually exclusive
in an entry.

Qualifier /frequency=
Definition frequency of the occurrence of a feature
Value format text representing the proportion of a population carrying the
feature expressed as a fraction
Example /frequency="23/108"
/frequency="1 in 12"
/frequency=".85"

Qualifier /function=
Definition function attributed to a sequence
Value format "text"
Example function="essential for recognition of cofactor"
Comment /function is used when the gene name and/or product name do not
convey the function attributable to a sequence.

Qualifier /gap_type=
Definition type of gap connecting components in records of a genome assembly,
or the type of biological gap in a record that is part of a genome
assembly;
Value format "between scaffolds", "within scaffold", "telomere", "centromere",
"short arm", "heterochromatin", "repeat within scaffold",
"repeat between scaffolds", "unknown"
Example /gap_type="between scaffolds"
/gap_type="within scaffold"
Comment This qualifier is used only for assembly_gap features and its values
are controlled by the AGP Specification version 2.0:
https://www.ncbi.nlm.nih.gov/assembly/agp/AGP_Specification/
Please also visit: http://www.insdc.org/controlled-vocabulary-gaptype-qualifier

Qualifier /gene_synonym=
Definition synonymous, replaced, obsolete or former gene symbol
Value format "text"
Example /gene_synonym="Hox-3.3"
in a feature where /gene="Hoxc6"
Comment used where it is helpful to indicate a gene symbol synonym;
when used, a primary gene symbol must always be indicated
in /gene or a /locus_tag must be used.

Qualifier /germline
Definition the sequence presented in the entry has not undergone somatic
rearrangement as part of an adaptive immune response; it is the
unrearranged sequence that was inherited from the parental
germline
Value format none
Example /germline
Comment /germline should not be used to indicate that the source of
the sequence is a gamete or germ cell;
/germline and /rearranged cannot be used in the same source
feature;
/germline and /rearranged should only be used for molecules that
can undergo somatic rearrangements as part of an adaptive immune
response; these are the T-cell receptor (TCR) and immunoglobulin
loci in the jawed vertebrates, and the unrelated variable
lymphocyte receptor (VLR) locus in the jawless fish (lampreys
and hagfish);
/germline and /rearranged should not be used outside of the
Craniata (taxid=89593)

Qualifier /haplogroup=
Definition name for a group of similar haplotypes that share some
sequence variation. Haplogroups are often used to track
migration of population groups.
Value format "text"
Example /haplogroup="H*"

Qualifier /haplotype=
Definition name for a combination of alleles that are linked together
on the same physical chromosome. In the absence of
recombination, each haplotype is inherited as a unit, and may
be used to track gene flow in populations.
Value format "text"
Example /haplotype="Dw3 B5 Cw1 A1"

Qualifier /inference=
Definition a structured description of non-experimental evidence that supports
the feature identification or assignment.
Value format "[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]"
where CATEGORY is one of the following:
"COORDINATES" support for the annotated coordinates
"DESCRIPTION" support for a broad concept of function such as that
based on phenotype, genetic approach, biochemical function, pathway
information, etc.
"EXISTENCE" support for the known or inferred existence of the product
where TYPE is one of the following:
"non-experimental evidence, no additional details recorded"
"similar to sequence"
"similar to AA sequence"
"similar to DNA sequence"
"similar to RNA sequence"
"similar to RNA sequence, mRNA"
"similar to RNA sequence, EST"
"similar to RNA sequence, other RNA"
"profile"
"nucleotide motif"
"protein motif"
"ab initio prediction"
"alignment"
where the optional text "(same species)" is included when the
inference comes from the same species as the entry.
where the optional "EVIDENCE_BASIS" is either a reference to a
database entry (including accession and version) or an algorithm
(including version) , eg 'INSD:AACN010222672.1', 'InterPro:IPR001900',
'ProDom:PD000600', 'Genscan:2.0', etc. and is structured
"[ALGORITHM][:EVIDENCE_DBREF[,EVIDENCE_DBREF]*[,...]]"
Example /inference="COORDINATES:profile:tRNAscan:2.1"
/inference="similar to DNA sequence:INSD:AY411252.1"
/inference="similar to RNA sequence, mRNA:RefSeq:NM_000041.2"
/inference="similar to DNA sequence (same
species):INSD:AACN010222672.1"
/inference="protein motif:InterPro:IPR001900"
/inference="ab initio prediction:Genscan:2.0"
/inference="alignment:Splign:1.0"
/inference="alignment:Splign:1.26p:RefSeq:NM_000041.2,INSD:BC003557.1"
Comment /inference="non-experimental evidence, no additional details
recorded" was used to replace instances of
/evidence=NOT_EXPERIMENTAL in December 2005; any database ID
can be used in /inference= qualifier; recommendations for
choice of resource acronym for[EVIDENCE_BASIS] are provided in
the /inference qualifier vocabulary recommendation document
(http://www.insdc.org/inference.html);

Qualifier /isolation_source=
Definition describes the physical, environmental and/or local
geographical source of the biological sample from which
the sequence was derived
Value format "text"
Examples /isolation_source="rumen isolates from standard
Pelleted ration-fed steer #67"
/isolation_source="permanent Antarctic sea ice"
/isolation_source="denitrifying activated sludge from
carbon_limited continuous reactor"
Comment used only with the source feature key;
source feature keys containing an /environmental_sample
qualifier should also contain an /isolation_source
qualifier; the /country qualifier should be used to
describe the country and major geographical sub-region.

Qualifier /lab_host=
Definition scientific name of the laboratory host used to propagate the
source organism from which the sequenced molecule was obtained
Value format "text"
Example /lab_host="Gallus gallus"
/lab_host="Gallus gallus embryo"
/lab_host="Escherichia coli strain DH5 alpha"
/lab_host="Homo sapiens HeLa cells"
Comment the full binomial scientific name of the host organism should
be used when known; extra conditional information relating to
the host may also be included

Qualifier /locus_tag=
Definition a submitter-supplied, systematic, stable identifier for a gene
and its associated features, used for tracking purposes
Value Format "text"(single token)
but not "<1-5 letters><5-9 digit integer>[.<integer>]"
Example /locus_tag="ABC_0022"
/locus_tag="A1C_00001"
Comment /locus_tag can be used with any feature that /gene can be used with;
identical /locus_tag values may be used within an entry/record,
but only if the identical /locus_tag values are associated
with the same gene; in all other circumstances the /locus_tag
value must be unique within that entry/record. Multiple /locus_tag
values are not allowed within one feature for entries created
after 15-OCT-2004.
If a /locus_tag needs to be re-assigned the /old_locus_tag qualifier
should be used to store the old value. The /locus_tag value should
not be in a format which resembles INSD accession numbers,
accession.version, or /protein_id identifiers.

Qualifier /macronuclear
Definition if the sequence shown is DNA and from an organism which
undergoes chromosomal differentiation between macronuclear and
micronuclear stages, this qualifier is used to denote that the
sequence is from macronuclear DNA.
Value format none
Example /macronuclear

Qualifier /mating_type=
Definition mating type of the organism from which the sequence was
obtained; mating type is used for prokaryotes, and for
eukaryotes that undergo meiosis without sexually dimorphic
gametes
Value format "text"
Examples /mating_type="MAT-1"
/mating_type="plus"
/mating_type="-"
/mating_type="odd"
/mating_type="even"
Comment /mating_type="male" and /mating_type="female" are
valid in the prokaryotes, but not in the eukaryotes;
for more information, see the entry for /sex.

Qualifier /mobile_element_type=
Definition type and name or identifier of the mobile element which is
described by the parent feature
Value format "<mobile_element_type>[:<mobile_element_name>]" where
mobile_element_type is one of the following:
"transposon", "retrotransposon", "integron",
"insertion sequence", "non-LTR retrotransposon",
"SINE", "MITE", "LINE", "other".
Example /mobile_element_type="transposon:Tnp9"
Comment /mobile_element_type is legal on mobile_element feature key only.
Mobile element should be used to represent both elements which
are currently mobile, and those which were mobile in the past.
Value "other" requires a mobile_element_name.

Qualifier /mod_base=
Definition abbreviation for a modified nucleotide base
Value format modified_base
Example /mod_base=m5c
Comment modified nucleotides not found in the restricted vocabulary
list can be annotated by entering '/mod_base=OTHER' with
'/note="name of modified base"'

Qualifier /mol_type=
Definition in vivo molecule type of sequence
Value format "genomic DNA", "genomic RNA", "mRNA", "tRNA", "rRNA",
"other RNA", "other DNA", "transcribed RNA", "viral cRNA",
"unassigned DNA", "unassigned RNA"
Example /mol_type="genomic DNA"
Comment all values refer to the in vivo or synthetic molecule for
primary entries and the hypothetical molecule in Third Party
Annotation entries; the value "genomic DNA" does not imply that
the molecule is nuclear (e.g. organelle and plasmid DNA should
be described using "genomic DNA"); ribosomal RNA genes should be
described using "genomic DNA"; "rRNA" should only be used if the
ribosomal RNA molecule itself has been sequenced; /mol_type is
mandatory on every source feature key; all /mol_type values
within one entry/record must be the same; values "other RNA" and
"other DNA" should be applied to synthetic molecules, values
"unassigned DNA", "unassigned RNA" should be applied where in
vivo molecule is unknown
Please also visit:
http://www.insdc.org/controlled-vocabulary-moltype-qualifier

Qualifier /ncRNA_class=
Definition a structured description of the classification of the
non-coding RNA described by the ncRNA parent key
Value format "TYPE"
Example /ncRNA_class="miRNA"
/ncRNA_class="siRNA"
/ncRNA_class="scRNA"
Comment TYPE is a term taken from the INSDC controlled vocabulary for ncRNA
classes (http://www.insdc.org/rna_vocab.html); on
15-Oct-2013, the following terms were valid:
"antisense_RNA"
"autocatalytically_spliced_intron"
"ribozyme"
"hammerhead_ribozyme"
"lncRNA"
"RNase_P_RNA"
"RNase_MRP_RNA"
"telomerase_RNA"
"guide_RNA"
"rasiRNA"
"scRNA"
"siRNA"
"miRNA"
"piRNA"
"snoRNA"
"snRNA"
"SRP_RNA"
"vault_RNA"
"Y_RNA"
"other"
ncRNA classes not yet in the INSDC /ncRNA_class controlled
vocabulary can be annotated by entering
'/ncRNA_class="other"' with '/note="[brief explanation of
novel ncRNA_class]"';

Qualifier /number=
Definition a number to indicate the order of genetic elements (e.g.,
exons or introns) in the 5' to 3' direction
Value format unquoted text (single token)
Example /number=4
/number=6B
Comment text limited to integers, letters or combination of integers and/or
letters represented as an unquoted single token (e.g. 5a, XIIb);
any additional terms should be included in /standard_name.
Example: /number=2A
/standard_name="long"

Qualifier /old_locus_tag=
Definition feature tag assigned for tracking purposes
Value Format "text" (single token)
Example /old_locus_tag="RSc0382"
/locus_tag="YPO0002"
Comment /old_locus_tag can be used with any feature where /gene is valid and
where a /locus_tag qualifier is present.
Identical /old_locus_tag values may be used within an entry/record,
but only if the identical /old_locus_tag values are associated
with the same gene; in all other circumstances the /old_locus_tag
value must be unique within that entry/record.
Multiple/old_locus_tag qualifiers with distinct values are
allowed within a single feature; /old_locus_tag and /locus_tag
values must not be identical within a single feature.

Qualifier /operon=
Definition name of the group of contiguous genes transcribed into a
single transcript to which that feature belongs.
Value format "text"
Example /operon="lac"

Qualifier /organism=
Definition scientific name of the organism that provided the
sequenced genetic material.
Value format "text"
Example /organism="Homo sapiens"
Comment the organism name which appears on the OS or ORGANISM line
will match the value of the /organism qualifier of the
source key in the simplest case of a one-source sequence.

Qualifier /partial
Definition differentiates between complete regions and partial ones
Value format none
Example /partial
Comment not to be used for new entries from 15-DEC-2001;
use '<' and '>' signs in the location descriptors to
indicate that the sequence is partial.

Qualifier /PCR_primers=
Definition PCR primers that were used to amplify the sequence.
A single /PCR_primers qualifier should contain all the primers used
for a single PCR reaction. If multiple forward or reverse primers are
present in a single PCR reaction, multiple sets of fwd_name/fwd_seq
or rev_name/rev_seq values will be present.
Value format /PCR_primers="[fwd_name: XXX1, ]fwd_seq: xxxxx1,[fwd_name: XXX2,]
fwd_seq: xxxxx2, [rev_name: YYY1, ]rev_seq: yyyyy1,
[rev_name: YYY2, ]rev_seq: yyyyy2"
Example /PCR_primers="fwd_name: CO1P1, fwd_seq: ttgattttttggtcayccwgaagt,
rev_name: CO1R4, rev_seq: ccwvytardcctarraartgttg"
/PCR_primers=" fwd_name: hoge1, fwd_seq: cgkgtgtatcttact,
rev_name: hoge2, rev_seq: cg<i>gtgtatcttact"
/PCR_primers="fwd_name: CO1P1, fwd_seq: ttgattttttggtcayccwgaagt,
fwd_name: CO1P2, fwd_seq: gatacacaggtcayccwgaagt, rev_name: CO1R4,
rev_seq: ccwvytardcctarraartgttg"
Comment fwd_seq and rev_seq are both mandatory; fwd_name and rev_name are
both optional. Both sequences should be presented in 5'>3' order.
The sequences should be given in the IUPAC degenerate-base alphabet,
except for the modified bases; those must be enclosed within angle
brackets <>

Qualifier /phenotype=
Definition phenotype conferred by the feature, where phenotype is defined as a
physical, biochemical or behavioural characteristic or set of
characteristics
Value format "text"
Example /phenotype="erythromycin resistance"

Qualifier /plasmid=
Definition name of naturally occurring plasmid from which the sequence was
obtained, where plasmid is defined as an independently replicating
genetic unit that cannot be described by /chromosome or /segment
Value format "text"
Example /plasmid="C-589"

Qualifier /pop_variant=
Definition name of subpopulation or phenotype of the sample from which the sequence
was derived
Value format "text"
Example /pop_variant="pop1"
/pop_variant="Bear Paw"

Qualifier /protein_id=
Definition protein identifier, issued by International collaborators.
this qualifier consists of a stable ID portion (3+5 format
with 3 position letters and 5 numbers) plus a version number
after the decimal point.
Value format <identifier>
Example /protein_id="AAA12345.1"
Comment when the protein sequence encoded by the CDS changes, only
the version number of the /protein_id value is incremented;
the stable part of the /protein_id remains unchanged and as a
result will permanently be associated with a given protein;
this qualifier is valid only on CDS features which translate
into a valid protein.

Qualifier /proviral
Definition this qualifier is used to flag sequence obtained from a virus or
phage that is integrated into the genome of another organism
Value format none
Example /proviral

Qualifier /pseudo
Definition indicates that this feature is a non-functional version of the
element named by the feature key
Value format none
Example /pseudo
Comment The qualifier /pseudo should be used to describe non-functional
genes that are not formally described as pseudogenes, e.g. CDS
has no translation due to other reasons than pseudogenisation events.
Other reasons may include sequencing or assembly errors.
In order to annotate pseudogenes the qualifier /pseudogene= must be
used indicating the TYPE which can be taken from the INSDC controlled vocabulary
for pseudogenes.

Qualifier /pseudogene=
Definition indicates that this feature is a pseudogene of the element named
by the feature key
Value format "TYPE"
where TYPE is one of the following:
processed, unprocessed, unitary, allelic, unknown
Example /pseudogene="processed"
/pseudogene="unprocessed"
/pseudogene="unitary"
/pseudogene="allelic"
/pseudogene="unknown"
Comment TYPE is a term taken from the INSDC controlled vocabulary for pseudogenes
( http://www.insdc.org/documents/pseudogene-qualifier-vocabulary ):
processed: the pseudogene has arisen by reverse transcription of a
mRNA into cDNA, followed by reintegration into the genome. Therefore,
it has lost any intron/exon structure, and it might have a pseudo-polyA-tail.
unprocessed: the pseudogene has arisen from a copy of the parent gene by duplication
followed by accumulation of random mutation. The changes, compared to their
functional homolog, include insertions, deletions, premature stop codons, frameshifts
and a higher proportion of non-synonymous versus synonymous substitutions.
unitary: the pseudogene has no parent. It is the original gene, which is
functional is some species but disrupted in some way (indels, mutation,
recombination) in another species or strain.
allelic: a (unitary) pseudogene that is stable in the population but
importantly it has a functional alternative allele also in the population. i.e.,
one strain may have the gene, another strain may have the pseudogene.
MHC haplotypes have allelic pseudogenes.
unknown: the submitter does not know the method of pseudogenisation.

Qualifier /rearranged
Definition the sequence presented in the entry has undergone somatic
rearrangement as part of an adaptive immune response; it is not
the unrearranged sequence that was inherited from the parental
germline
Value format none
Example /rearranged
Comment /rearranged should not be used to annotate chromosome
rearrangements that are not involved in an adaptive immune
response;
/germline and /rearranged cannot be used in the same source
feature;
/germline and /rearranged should only be used for molecules that
can undergo somatic rearrangements as part of an adaptive immune
response; these are the T-cell receptor (TCR) and immunoglobulin
loci in the jawed vertebrates, and the unrelated variable
lymphocyte receptor (VLR) locus in the jawless fish (lampreys
and hagfish);
/germline and /rearranged should not be used outside of the
Craniata (taxid=89593)

Qualifier /recombination_class
Definition a structured description of the classification of recombination
hotspot region within a sequence
Value format "TYPE"
Example /recombination_class="meiotic recombination"
/recombination_class="chromosome_breakpoint"
Comment TYPE is a term taken from the INSDC controlled vocabulary for recombination
classes ( http://www.insdc.org/controlled-vocabulary-recombination-class );
on 15-OCT-2016, the following terms were valid:
meiotic_recombination
mitotic_recombination
non_allelic_homologous_recombination_region
chromosome_breakpoint
other
recombination classes not yet in the INSDC /recombination_class controlled
vocabulary can be annotated by entering /recombination_class="other" with
/note="[brief explanation of novel /recombination_class]";

Qualifier /replace=
Definition indicates that the sequence identified a feature's intervals is
replaced by the sequence shown in "text"; if no sequence is
contained within the qualifier, this indicates a deletion.
Value format "text"
Example /replace="a"
/replace=""

Qualifier /ribosomal_slippage
Definition during protein translation, certain sequences can program
ribosomes to change to an alternative reading frame by a
mechanism known as ribosomal slippage
Value format none
Example /ribosomal_slippage
Comment a join operator,e.g.: [join(486..1784,1787..4810)] should be used
in the CDS spans to indicate the location of ribosomal_slippage

Qualifier /rpt_unit_range=
Definition identity of a repeat range
Value format <base_range>
Example /rpt_unit_range=202..245
Comment used to indicate the base range of the sequence that constitutes
a repeated sequence specified by the feature keys oriT and
repeat_region; qualifiers /rpt_unit_range and /rpt_unit_seq
replaced qualifier /rpt_unit in December 2005

Qualifier /satellite=
Definition identifier for a satellite DNA marker, compose of many tandem
repeats (identical or related) of a short basic repeated unit;
Value format "<satellite_type>[:<class>][ <identifier>]"
where satellite_type is one of the following
"satellite", "microsatellite", "minisatellite"
Example /satellite="satellite: S1a"
/satellite="satellite: alpha"
/satellite="satellite: gamma III"
/satellite="microsatellite: DC130"
Comment many satellites have base composition or other properties
that differ from those of the rest of the genome that allows
them to be identified.
Please also visit: http://www.insdc.org/controlled-vocabulary-satellite-qualifier

Qualifier /serotype=
Definition serological variety of a species characterized by its
antigenic properties
Value format "text"
Example /serotype="B1"
Comment used only with the source feature key;
the Bacteriological Code recommends the use of the
term 'serovar' instead of 'serotype' for the
prokaryotes; see the International Code of Nomenclature
of Bacteria (1990 Revision) Appendix 10.B "Infraspecific
Terms".

Qualifier /serovar=
Definition serological variety of a species (usually a prokaryote)
characterized by its antigenic properties
Value format "text"
Example /serovar="O157:H7"
Comment used only with the source feature key;
the Bacteriological Code recommends the use of the
term 'serovar' instead of 'serotype' for prokaryotes;
see the International Code of Nomenclature of Bacteria
(1990 Revision) Appendix 10.B "Infraspecific Terms".

Qualifier /sex=
Definition sex of the organism from which the sequence was obtained;
sex is used for eukaryotic organisms that undergo meiosis
and have sexually dimorphic gametes
Value format "text"
Examples /sex="female"
/sex="male"
/sex="hermaphrodite"
/sex="unisexual"
/sex="bisexual"
/sex="asexual"
/sex="monoecious" [or monecious]
/sex="dioecious" [or diecious]
Comment /sex should be used (instead of /mating_type)
in the Metazoa, Embryophyta, Rhodophyta & Phaeophyceae;
/mating_type should be used (instead of /sex)
in the Bacteria, Archaea & Fungi;
neither /sex nor /mating_type should be used
in the viruses;
outside of the taxa listed above, /mating_type
should be used unless the value of the qualifier
is taken from the vocabulary given in the examples
above

Qualifier /specimen_voucher=
Definition identifier for the specimen from which the nucleic acid
sequenced was obtained
Value format /specimen_voucher="[<institution-code>:[<collection-code>:]]<specimen_id>"
Example /specimen_voucher="UAM:Mamm:52179"
/specimen_voucher="AMCC:101706"
/specimen_voucher="USNM:field series 8798"
/specimen_voucher="personal:Dan Janzen:99-SRNP-2003"
/specimen_voucher="99-SRNP-2003"
Comment the /specimen_voucher qualifier is intended to annotate a
reference to the physical specimen that remains after the
sequence has been obtained;
if the specimen was destroyed in the process of sequencing,
electronic images (e-vouchers) are an adequate substitute for a
physical voucher specimen; ideally the specimens will be
deposited in a curated museum, herbarium, or frozen tissue
collection, but often they will remain in a personal or
laboratory collection for some time before they are deposited in
a curated collection;
there are three forms of specimen_voucher qualifiers; if the
text of the qualifier includes one or more colons it is a
'structured voucher'; structured vouchers include
institution-codes (and optional collection-codes) taken from a
controlled vocabulary maintained by the INSDC that denotes the
museum or herbarium collection where the specimen resides;
Please also visit: http://www.insdc.org/controlled-vocabulary-specimenvoucher-qualifier

Qualifier /strain=
Definition strain from which sequence was obtained
Value format "text"
Example /strain="BALB/c"
Comment entries including /strain must not include
the /environmental_sample qualifier

Qualifier /sub_species=
Definition name of sub-species of organism from which sequence was
obtained
Value format "text"
Example /sub_species="lactis"

Qualifier /sub_strain=
Definition name or identifier of a genetically or otherwise modified
strain from which sequence was obtained, derived from a
parental strain (which should be annotated in the /strain
qualifier).sub_strain from which sequence was obtained
Value format "text"
Example /sub_strain="abis"
Comment If the parental strain is not given, this should
be annotated in the strain qualifier instead of sub_strain.
Either:
/strain="K-12"
/sub_strain="MG1655"
or:
/strain="MG1655"

Qualifier /transgenic
Definition identifies the source feature of the organism which was
the recipient of transgenic DNA.
Value format none
Example /transgenic
Comment transgenic sequences must have at least two source feature keys;
the source feature key having the /transgenic qualifier must
span the whole sequence; the source feature carrying the
/transgenic qualifier identifies the main organism of the entry,
this determines: a) the name displayed in the organism lines,
b) if no translation table is specified, the translation table;
only one source feature with /transgenic is allowed in an entry;
the /focus and /transgenic qualifiers are mutually exclusive in
an entry.

Qualifier /translation=
Definition automatically generated one-letter abbreviated amino acid
sequence derived from either the universal genetic code or the
table as specified in /transl_table and as determined by an
exception in the /transl_except qualifier
Value format IUPAC one-letter amino acid abbreviation, "X" is to be used
for AA exceptions.
Example /translation="MASTFPPWYRGCASTPSLKGLIMCTW"
Comment to be used with CDS feature only; this is a mandatory qualifier
in the CDS feature key except where /pseudogene="TYPE" or /pseudo
is shown; see /transl_table for definition and location of genetic
code tables.

Qualifier /transl_except=
Definition translational exception: single codon the translation of which
does not conform to genetic code defined by /organism or
/transl_table.
Value format (pos:location,aa:<amino_acid>) where amino_acid is the
amino acid coded by the codon at the base_range position
Example /transl_except=(pos:213..215,aa:Trp)
/transl_except=(pos:1017,aa:TERM)
/transl_except=(pos:2000..2001,aa:TERM)
/transl_except=(pos:X22222:15..17,aa:Ala)
Comment if the amino acid is not on the restricted vocabulary list use
e.g., '/transl_except=(pos:213..215,aa:OTHER)' with
'/note="name of unusual amino acid"';
for modified amino-acid selenocysteine use three letter code
'Sec' (one letter code 'U' in amino-acid sequence)
/transl_except=(pos:1002..1004,aa:Sec);
for partial termination codons where TAA stop codon is
completed by the addition of 3' A residues to the mRNA
either a single base_position or a base_range is used, e.g.
if partial stop codon is a single base:
/transl_except=(pos:1017,aa:TERM)
if partial stop codon consists of two bases:
/transl_except=(pos:2000..2001,aa:TERM) with
'/note='stop codon completed by the addition of 3' A residues
to the mRNA'.

Qualifier /trans_splicing
Definition indicates that exons from two RNA molecules are ligated in
intermolecular reaction to form mature RNA
Value format none
Example /trans_splicing
Comment should be used on features such as CDS, mRNA and other features
that are produced as a result of a trans-splicing event. This
qualifier should be used only when the splice event is indicated in
the "join" operator, eg join(complement(69611..69724),139856..140087)

Qualifier /type_material=
Definition indicates that the organism from which this sequence was obtained is
a nomenclatural type of the species (or subspecies) corresponding with
the /organism identified in the sequence entry
Value format "<type-of-type> of <organism name>"
where type-of-type is one of the following:
type strain, neotype strain, holotype, paratype, neotype, allotype, hapanotype,
syntype, lectotype, paralectotype, isotype, epitype, isosyntype, ex-type,
reference strain, type material;
Example /type_material="type strain of Escherichia coli"
/type_material="holotype of Cercopitheus lomamiensis"
/type_material="paratype of Cercopitheus lomamiensis"
Comment <type-of-type> is taken from a controlled vocabularly, listed above.
<organism name> should be listed as the scientific name
(or as a synonym) at the species (or subsopecies) node in the taxonomy database.
Usage of /type_material will start in the second half of 2014.

7.4 Appendix IV: Controlled vocabularies

This appendix contains information on the restricted vocabulary fields used in
the Feature Table. The information contained in this appendix is subject to
change, please contact the database staff for the most recent information
concerning controlled vocabularies. This appendix is organized as follows:
Authority The organization with authority to define the vocabulary
Reference Publications of (or about) the vocabulary
Contact Name of database staff responsible for maintaining
the database copy of the vocabulary
Scope Feature Table qualifiers which take members of this vocabulary
as values
Listing A listing of the current vocabulary with definitions or
explanations
This appendix includes reference lists for the following controlled vocabulary
fields:
- Nucleotide base codes (IUPAC)
- Modified base abbreviations
- Amino acid abbreviations
- Modified and unusual Amino Acids
- Genetic Code Tables
- Country Names

7.4.1 Nucleotide base codes (IUPAC)

Authority Nomenclature Committee of the International Union of
Biochemistry
Reference Cornish-Bowden, A. Nucl Acid Res 13, 3021-3030 (1985)
Contact EMBL-EBI
Scope Location descriptors
Listing
Symbol Meaning
------ -------
a a; adenine
c c; cytosine
g g; guanine
t t; thymine in DNA; uracil in RNA
m a or c
r a or g
w a or t
s c or g
y c or t
k g or t
v a or c or g; not t
h a or c or t; not g
d a or g or t; not c
b c or g or t; not a
n a or c or g or t

7.4.6 Country Names

7.4.7 Announces

Additional controlled vocabulary terms for qualifier values might be added
outside of the cycle of the Feature Table document release. See also www.insdc.org
with controlled vocabularies in the Feature Table document.
From December 2016 a complete list of the genetic codes will also be maintained outside
of the cycle of the Feature Table document release at:
http://www.insdc.org/genetic-code-tables